Category: technology

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Community science: what’s the value?

ONE SCIENTIST OFFERS HER PERSPECTIVE

By Sotiria Boutsi, Intern

I am PhD student at Harper Adams University with MSc in Conservation Biology, currently doing a professional internship at the Museum of Natural History in the Public Engagement office. My PhD uses genomic data to study speciation in figs and fig wasps.

For most of our history, humans have been observational creatures. Studying the natural world has been an essential tool for survival, a form of entertainment, and has provided the backbone for various legends and myths. Yet modern humans are rapidly losing practice when it comes to environmental observation. As more and more of us relocate to busy urban environments, we find ourselves with little to no time to spend outdoors. Knowledge of the natural world is rapidly becoming the purview of professionals — but it doesn’t have to be this way…

Community science is a term that describes scientific research activities conducted by amateurs, often involving observation or simple computational tasks. Many citizen science projects target schools or families, but everyone is a welcome participant. The purpose of such projects, which run all around the world, is to encourage non-professionals to get involved in science in a fun, voluntary manner, while also collecting data that are valuable for scientific research.

One of the most common forms of community science is biodiversity monitoring. Biodiversity monitoring projects invite people with various levels of expertise to record observations of different species in their local area, and upload evidence like photographs and sound recordings to a user-friendly database. In doing so, they also provide important monitoring data to scientists, like information about the date and location of wildlife sightings.

The Asian Ladybeetle (Harmonia axyridis) was first spotted in the UK in 2004 and since then it has become very common. It is considered one of the most widespread invasive species in the world, with introductions throughout Europe, North and South America, as well as South Africa. Reported observations through the UK Ladybird Survey (Enter ladybird records | iRecord) can help us monitor the spread of this insect and see how other, native species respond to its presence.

There are a variety of mobile apps and online platforms for reporting observations, with some specialising in particular groups of organisms like plants or birds. From the raw data that is uploaded to these platforms, species can be identified through a range of different methods:

  1. Automatic identification from uploaded evidence – often using techniques like image/sound analysis or machine learning
  2. Community feedback – multiple users can view uploaded evidence and make suggestions about which species have been recorded
  3. Direct use of users’ own suggestions – for users who are more experienced with species identification

But are these data actually used by scientists? Although individual contributions to community science projects may seem to be of minor importance, when considered collectively they act as extremely valuable records. Having distribution data for species can help us understand their habitat preferences, and also enable us to monitor invasive organisms. Moreover, long-term data can inform us about species’ responses to changes in their environments, whether that is habitat alteration or climate change. Science is driven by the accumulation of data, and citizen science projects can provide just that.

Biodiversity monitoring through citizen science projects encourage us to notice the tiny beings around us, like this beautifully coloured shiny Green Dock Beetle (Gastrophysa viridula). Moreover, recording common species like the European Honeybee (Apis mellifera) over different years can reveal temporal patterns, like early arrival of spring.

In addition to the benefits to the scientific field, community science projects can also be of huge value to their participants. Firstly, engaging in such activities can help us re-establish our relationship with the wildlife in our immediate environment — we might finally learn to identify common species in our local area, or discover new species that we never realised were so close by. It is surprising how many species we can even find in our own gardens! Moreover, community science events, like biodiversity-monitoring “BioBlitzes”, encourage people from different backgrounds to work together, strengthening local communities and encouraging environmental protection.

Oxford University is currently running the community science project “Oxford Plan Bee“, focusing on solitary bees. The project is creating a network of bee hotels: small boxes with branches and wooden cavities where harmless, solitary bees can rest. The hotels are spread throughout the city, and locals are invited to observe the bee hotels, take photos, and send in their findings.

Overall, community science is as much about being an active participant in the community as it is about doing science. These projects are a celebration of both collective contributions and individual growth. More than anything, they are a chance to pause and notice the little things that keep our planet running.

Want to get involved? Here is a selection of my favourite citizen science projects…

Recording species observations – global:

Recording species observations – UK-based:

Bioblitz events:

Read more:

How a Citizen Science project helped solve a mystery of UK butterflies: Painted Lady migration secrets unveiled – News and events, University of York

Citizen Science Hub – British Ecological Society

Citizen Science Platforms | SpringerLink

Citizen Science in the Natural Sciences | SpringerLink

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The Roundup on The Great Debate – Do We Need a New Agricultural Revolution?

Post by Dr Caroline Wood

How can we meet the challenge of feeding 10 billion people by 2050 whilst simultaneously addressing climate change, impoverished soils, mass extinctions and unsustainable pollution?

On 20th October, Oxford University Museum of Natural History hosted The Great Debate – an anniversary celebration of the Museum’s Great Debate in 1860, on Darwin’s Theory of Evolution. During this special event, the panel and audience (both in-person and live-streamed) discussed issues, opportunities and tensions relating to the future of food production. By the end of the evening, it was clear that we won’t be able to rely on ‘quick fixes’. Instead, we will need a whole-scale revolution at multiple levels: in our fields, on our plates, and in our attitudes. 

Panel Speakers

Lord John Krebs (Chair) – Former chairman of the Natural Environment Research Committee and Adaptation to Climate Change Committee

Helen Browning – Chief Executive of the Soil Association

Professor Sir Charles Godfray – Director of the Oxford Martin School

Stuart Roberts – Deputy President of the National Farmers Union (NFU)

In our fields

With global food demand estimated to increase by 35% to 56% between 2010 and 2050, it is unquestionable that we will need to keep producing more food. Although the prospect seems daunting, Helen Browning outlined the potential of new technologies to boost yields, including hydroponics and vertical farming; robots that can perform crop care and harvesting; and genetic technologies such as gene editing. However, she warned that the UK is currently ‘way off the pace’, and would remain so until there is more investment in farmer-led research, innovation and knowledge-sharing opportunities. 

As Stuart Roberts pointed out, there are also significant opportunities to boost production simply by addressing inefficiencies and yield gaps. For instance, according to the NFU, if all the 270 million+ dairy animals worldwide were as efficient as UK dairy cows, we would only need 76 million to produce the same amount of milk. New market models, such as direct-to-consumer and digital technologies (e.g. blockchain), could also help reduce the 15% of food that the WWF estimate is wasted even before it leaves the farm. 

But will increased production come at the expense of damaging natural ecosystems? The new UK Agricultural Act aims to avoid this by providing farmers with a financial incentive to preserve ‘public goods’ including air quality, biodiversity, soil health, and flood mitigation. Sir Charles foresaw that the Agricultural Act will result in a ‘patchwork’ of different farming systems across the UK, each tailored to their locality, with some being highly productive and others more dedicated to public services. 

Debate Panel (Left to Right) – Lord John Krebs, Helen Browning, Stuart Roberts, Prof Sir Charles Godfrey

On our plates

Extensive research indicates that achieving net-zero carbon emissions will require a global reduction in meat consumption and a shift towards plant-based diets. But as Stuart noted, presenting consumers with only the extremes of a carnivorous diet and a vegan lifestyle is not helping this transition. Instead of focusing on binary choices, we should be more concerned with improving the meat we do eat. As consumers, we need to stop seeing food as a cheap, mass-produced commodity, and be prepared to pay a price that will compensate for the development of production systems that are more in harmony with nature. Helen agreed that only by paying more for food can we allow farmers to escape the stranglehold of contracts that pressure them to produce as much as possible, regardless of the environmental cost. However, as Stuart pointed out, to avoid higher prices leading to food poverty, it will be necessary to tackle income poverty first. To this end, he cited Food Foundation research which reveals that the poorest 10% of households would have to spend 76% of their disposable income to meet current diet recommendations.

In our minds

Farmers are critical actors in the global response to climate change, but all too often they are portrayed as villains. Stereotypes regularly cast farmers as chemical lovers who rip up hedgerows and mistreat animals. Instead, we need to recognise and celebrate the farmers who are trying to be part of the solution, including those embracing regenerative farming methods such as pasture cropping, agroforestry, no-till farming and undersowing. Overall, if we want more farmers to become innovators, we need to support them – and as consumers, we can make that choice every time we shop.

The Huxley Room at the Oxford Natural History Museum where the original Great Debate took place in 1860.

Dr Caroline Wood works as a Communications Officer for Oxford Population Health, a department at Oxford University that specialises in global health studies. She is also a freelance science writer, focusing on sustainability, food science and packaging issues. When she is not writing, she enjoys visiting museums (including OUMNH obviously!), hillwalking and painting (badly). 

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Attack of the Space Spider

Wondrous things have been going on in the Charles Lyell Project recently! I have been using a really cool piece of kit that uses structured light scanning to produce a 3D image of the fossils. The best thing is it’s called the Space Spider and looks like a gadget from Star Trek, maybe a high tech whisk or iron. Using this, and a very helpful assistant, you can produce a complete 3D image in 15 – 40 minutes depending on how large and complicated the specimen is and how many times you mess up (assistant sold separately).

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This is what you can create!

So for anyone who has, or now wants to have, a Space Spider (and the Artec Studio 11 Professional software that goes with it) this is how I used it…

1. Be patient

It takes quite a long time to warm up. It will say it has 10 minutes left which is actually about an hour. Bring a book or something to do. It is worth the wait.

If you are dealing with large specimens or complex specimens the scans will take up a lot of memory meaning occasionally the program will freeze.

2. Scan as much as possible

In your first scan you want to cover as much of the specimen as possible to make it easier when it comes to alignment later. We started off with two complete scans of the specimen in two different orientations, adding more later if necessary, unless it was obvious we had missed something.

Using the real time fusion setting makes it much easier to see when scanning.

3. Just because the machine is high tech doesn’t mean you need to be

It is easier to put the specimen on something that rotates such as the turntable baker’s use to ice cakes. We did not have this so instead we used a plastic box. However we noticed that we were losing tracking more often than we were before. It was because of the box being reflective (this was also seen when it reflected off rings). So we used powder free vinyl gloves to cover the box solving the problem.

IMG_0331.JPG
High tech meets very low tech

4. Get rid of the floaters

There is often some noise generated by the scan, whether it has picked up a bit of table or you accidentally scanned your finger when turning the box. This can be removed in the editing part of the software. We found using the lasso or rectangle to be the easiest. Doing this after every scan rather than after scanning is complete will make it easier.

Don’t worry about getting every single one, you can get rid of the rest later using the small object filter!

5. Alignment

It was usually a bit of trial and error with the alignment but if you have done two really good scans you can get it in one go. To align you set similar points on the two scans, it is best to aim for 3 but has worked with 2.

One silly mistake that is really easy to make (especially when you are tired) is putting the points on and pressing apply without actually aligning them. Back to the beginning you go!

ALIGN.jpg
Three points used to align the two scans

6. The thing you have to do and I don’t know why

Globally register the scans. I don’t know what it means or what it does but you have to do it before you can move on.

Don’t question, just do.

7. The rest of the tools

After globally registering your scans you can use the other tools.

First: Fast fusion. There are two other types of fusion, sharp and smooth, but this one is much faster and gives good results. Only fuse the scans without texture as you add this later.

Second: Small object filter. This gets rid of any pesky floaters still remaining after fusing.

no-texture
Specimen before hole filling, looking pretty good though

Third: Hole filler. Does what it says on the tin, fills any holes that are in the scan. This is particularly useful for apertures of gastropods as the scanner can’t always get into them.

8. Weird lumps

So you have fused your scans, got rid of holes and the last standing floater but oh no there’s a weird lump on your scan that’s not on your specimen, disaster! Don’t fear the smoothing brush is here. In editor there is a smoothing brush (located above erase) which you can adjust the size of and get rid of any pesky lumps and bumps.

9. Going back

If none of the above has worked to fill a gap or there’s an odd bit go back and add another scan. Then repeat stages 2-8. If not move on and feel proud that you got it in one go.

10. Adding texture

At this stage you should have a beautiful 3D model but it will be one solid colour, not like the outside of the specimen at all. So to get the specimen looking its best you go to the texture tab. Highlight the scans that you want to use. The standard and recommended settings work well for this.

It will save your project. This is the point you feel glad that someone remembered to save it. This bit takes a little while (not more than 5 minutes) so you may want to refer to the book or activity from before.

You can use the sidebar to change brightness, saturation and other fun things. The most entertaining setting to play with is the hue; you can make the specimens any colour (even making them look mouldy).

Once you are happy, apply it.

With texture.jpg
This is with texture added

11. Save again

Pat yourself on the back for remembering.

12. Export

Exporting scans in a PLY format will give you the scans without the texture.

I recommend exporting meshes which has the texture export format as jpg. This gives you a PLY file with texture this time.

13. You’re done

Well done you have reached the end. My record was 15 minutes.

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Just a few final tips:

  • Remember to press apply so you don’t lose the changes you have made
  • Try to remember to save as you go along
  • Play with the settings until you find what you need
  • Don’t be afraid of trial and error
  • If it freezes just give it a minute, it usually comes back.